[R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission bwt 1.1.0
Joris Meys
Jori@@Mey@ @ending from ugent@be
Wed May 30 17:17:04 CEST 2018
Hi Khoong,
I'm going to address the elephant in the room: your package is not ready
for CRAN, and I'm not even sure CRAN is the right place for that code.
There's two large issues with your package, next to the license problem
Hugh pointed out already:
1. R code needs to be in subdirectory R, the Rd file needs to be in a
subdirectory called man. In the tar.gz file, both are in the main folder.
That's never going to work.
2. Your Rd file is seriously messed up. The name and alias contain what
should be the title, the title isn't filled in. I suggest you take a look
at roxygen2 to help you write the documentation, or go through Writing R
extensions again to check the details on the man pages.
\name{bwt}
\alias{ibwt}
will at least get the one warning about undocumented objects away.
3. The package in its entirity is 2 rather short functions. I'm not from
CRAN, but I don't know if that would pass the "non-trivial contribution"
test. You might want to think about a package that could import your code
rather than submitting a separate package. Not saying the code is not
valuable or the package has no place on CRAN, but you might get questions
on that and then it's better to be prepared with a good answer as to why
this really should be on CRAN.
Your error otoh looks like something that is not your fault. As far as I
know, having a test suite using testthat is not obligatory for a CRAN
package. Yet, CRAN did try to run the tests and errored because it couldn't
find any. I'll raise that at R-devel and see what's going on there.
Nevertheless, adding a few tests would be a good idea. testthat lets you do
that rather easily, and you can find more information in the vignettes of
that package and Hadley's book on writing packages.
Hope this helps
Cheers
Joris
On Wed, May 30, 2018 at 4:52 PM, Hugh Parsonage <hugh.parsonage using gmail.com>
wrote:
> Hi,
>
> There are a few problems with the submission. Probably more than can
> be resolved by people on the mailing list. Speaking generally, a
> WARNING in a CRAN check is something that *must* be fixed, rather than
> something which you can just acknowledge. The two warnings that you
> mentioned are that you probably have (in your DESCRIPTION file)
>
> License: GNU General Public License v3.0
>
> when you should have
>
> License: GPL-3
>
> The second warning is about undocumented code objects. You can choose
> not to export them, but if you do export them as you currently are,
> you will need to document them.
>
> I notice that there are other problems too: consult the links in the
> auto-generated email from CRAN, see the 00check file. You should fix
> every problem until there are no ERRORS, WARNINGS, or NOTEs.
>
>
> Best.
>
> On 31 May 2018 at 00:03, khoong Wei Hao <khoongweihao using hotmail.com> wrote:
> > Hi Everyone,
> >
> > I encountered an issue during my submission of my package (see original
> message below).
> >
> > I ran checks and tests with testthat::test_dir("tests/") and
> devtoos::check(), and all seemed fine except some issues with undocumented
> objects which I did note in the .Rd file, and the documentation appeared in
> the console as I ran the package. The following is my R console output:
> >
> >> devtools::check()
> > Updating bwt documentation
> > Loading bwt
> > First time using roxygen2. Upgrading automatically...
> > Warning: The existing 'NAMESPACE' file was not generated by roxygen2,
> and will not be overwritten.
> > Setting env vars ------------------------------
> ----------------------------------------------------------------------
> > CFLAGS : -Wall -pedantic
> > CXXFLAGS: -Wall -pedantic
> > Building bwt ------------------------------
> --------------------------------------------------------------------------
> > "C:/PROGRA~1/R/R-33~1.2/bin/x64/R" --no-site-file --no-environ
> --no-save --no-restore --quiet CMD build \
> > "C:\Users\khoongwh\Documents\bwt" --no-resave-data --no-manual
> >
> > * checking for file 'C:\Users\khoongwh\Documents\bwt/DESCRIPTION' ... OK
> > * preparing 'bwt':
> > * checking DESCRIPTION meta-information ... OK
> > * checking for LF line-endings in source and make files
> > * checking for empty or unneeded directories Removed empty directory
> 'bwt/man'
> > Removed empty directory 'bwt/tests/testthat'
> > * building 'bwt_1.1.0.tar.gz'
> >
> > Setting env vars ------------------------------
> ----------------------------------------------------------------------
> > _R_CHECK_CRAN_INCOMING_ : FALSE
> > _R_CHECK_FORCE_SUGGESTS_: FALSE
> > Checking bwt ------------------------------
> --------------------------------------------------------------------------
> > "C:/PROGRA~1/R/R-33~1.2/bin/x64/R" --no-site-file --no-environ
> --no-save --no-restore --quiet CMD check \
> > "C:\Users\khoongwh\AppData\Local\Temp\RtmpKmUMRO/bwt_1.1.0.tar.gz"
> --as-cran --timings --no-manual
> >
> > * using log directory 'C:/Users/khoongwh/AppData/
> Local/Temp/RtmpKmUMRO/bwt.Rcheck'
> > * using R version 3.3.2 (2016-10-31)
> > * using platform: x86_64-w64-mingw32 (64-bit)
> > * using session charset: ISO8859-1
> > * using options '--no-manual --as-cran'
> > * checking for file 'bwt/DESCRIPTION' ... OK
> > * checking extension type ... Package
> > * this is package 'bwt' version '1.1.0'
> > * package encoding: UTF-8
> > * checking package namespace information ... OK
> > * checking package dependencies ... OK
> > * checking if this is a source package ... OK
> > * checking if there is a namespace ... OK
> > * checking for .dll and .exe files ... OK
> > * checking for hidden files and directories ... OK
> > * checking for portable file names ... OK
> > * checking whether package 'bwt' can be installed ... OK
> > * checking package directory ... OK
> > * checking DESCRIPTION meta-information ... WARNING Non-standard license
> specification:
> > GNU General Public License v3.0
> > Standardizable: FALSE
> > * checking top-level files ... OK
> > * checking for left-over files ... OK
> > * checking index information ... OK
> > * checking package subdirectories ... OK
> > * checking R files for non-ASCII characters ... OK
> > * checking R files for syntax errors ... OK
> > * checking whether the package can be loaded ... OK
> > * checking whether the package can be loaded with stated dependencies
> ... OK
> > * checking whether the package can be unloaded cleanly ... OK
> > * checking whether the namespace can be loaded with stated dependencies
> ... OK
> > * checking whether the namespace can be unloaded cleanly ... OK
> > * checking loading without being on the library search path ... OK
> > * checking dependencies in R code ... OK
> > * checking S3 generic/method consistency ... OK
> > * checking replacement functions ... OK
> > * checking foreign function calls ... OK
> > * checking R code for possible problems ... OK
> > * checking for missing documentation entries ... WARNING Undocumented
> code objects:
> > 'bwt' 'ibwt'
> > All user-level objects in a package should have documentation entries.
> > See chapter 'Writing R documentation files' in the 'Writing R
> Extensions' manual.
> > * checking examples ... NONE
> > * checking for unstated dependencies in 'tests' ... OK
> > * checking tests ...
> > Running 'testthat.R'
> > Warning message:
> > running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD BATCH
> --vanilla "testthat.R" "testthat.Rout"' had status 1 ERROR Running the
> tests in 'tests/testthat.R' failed.
> > Last 13 lines of output:
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > > library(testthat)
> > Warning message:
> > package 'testthat' was built under R version 3.3.3
> > > library(bwt)
> > >
> > > test_check("bwt")
> > Error: No tests found for bwt
> > Execution halted
> > * DONE
> >
> > Status: 1 ERROR, 2 WARNINGs
> > See
> > 'C:/Users/khoongwh/AppData/Local/Temp/RtmpKmUMRO/bwt.
> Rcheck/00check.log'
> > for details.
> >
> > R CMD check results
> > 1 error | 2 warnings | 0 notes
> > checking tests ... ERROR
> > Running the tests in 'tests/testthat.R' failed.
> > Last 13 lines of output:
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > > library(testthat)
> > Warning message:
> > package 'testthat' was built under R version 3.3.3
> > > library(bwt)
> > >
> > > test_check("bwt")
> > Error: No tests found for bwt
> > Execution halted
> >
> > checking DESCRIPTION meta-information ... WARNING Non-standard license
> specification:
> > GNU General Public License v3.0
> > Standardizable: FALSE
> >
> > checking for missing documentation entries ... WARNING Undocumented code
> objects:
> > 'bwt' 'ibwt'
> > All user-level objects in a package should have documentation entries.
> > See chapter 'Writing R documentation files' in the 'Writing R
> Extensions' manual.
> >
> > May I know how can I proceed? I am kind of lost a this pint in time,
> even after looking up CRAN's documentations.. If it helps, attached in this
> email is my .tar.gz file which I have submitted earlier.
> >
> > Thank you and I apologize for any inconvenience that I may have caused..
> >
> > Warmest Regards,
> >
> > Wei Hao Khoong (Mr)
> >
> > -----Original Message-----
> > From: Uwe.Ligges using R-Project.org <Uwe.Ligges using R-Project.org>
> > Sent: Wednesday, 30 May 2018 12:11 AM
> > To: khoongweihao using hotmail.com
> > Cc: CRAN-submissions using R-project.org
> > Subject: [CRAN-pretest-archived] CRAN submission bwt 1.1.0
> >
> > Dear maintainer,
> >
> > package bwt_1.1.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> >
> >
> > Status: 3 WARNINGs, 3 NOTEs
> > Debian: <https://win-builder.r-project.org/incoming_pretest/
> bwt_1.1.0_20180529_101440/Debian/00check.log>
> > Status: 3 WARNINGs, 3 NOTEs
> >
> >
> >
> > Please fix all problems and resubmit a fixed version via the webform.
> > If you are not sure how to fix the problems shown, please ask for help
> on the R-package-devel mailing list:
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> > If you are fairly certain the rejection is a false positive, please
> reply-all to this message and explain.
> >
> > More details are given in the directory:
> > <https://win-builder.r-project.org/incoming_pretest/
> bwt_1.1.0_20180529_101440/>
> > The files will be removed after roughly 7 days.
> >
> > No strong reverse dependencies to be checked.
> >
> > Best regards,
> > CRAN teams' auto-check service
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
--
Joris Meys
Statistical consultant
Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>
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